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DOE OSTI2022

Nonsynonymous amino acid changes in the α-chain of complement component 5 influence longitudinal susceptibility to Plasmodium falciparum infections and severe malarial anemia in kenyan children

Background: Severe malarial anemia (SMA; Hb < 5.0 g/dl) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission regions such as western Kenya. Methods: We investigated the relationship between two novel complement component 5 (C5) missense mutations [rs17216529:C>T, p(Val145Ile) and rs17610:C>T, p(Ser1310Asn)] and longitudinal outcomes of malaria in a cohort of Kenyan children (under 60 mos, n = 1,546). Molecular modeling was used to investigate the impact of the amino acid transitions on the C5 protein structure. Results: Prediction of the wild-type and mutant C5 protein structures did not reveal major changes to the overall structure. However, based on the position of the variants, subtle differences could impact on the stability of C5b. The influence of the C5 genotypes/haplotypes on the number of malaria and SMA episodes over 36 months was determined by Poisson regression modeling. Genotypic analyses revealed that inheritance of the homozygous mutant (TT) for rs17216529:C>T enhanced the risk for both malaria (incidence rate ratio, IRR = 1.144, 95%CI: 1.059–1.236, p = 0.001) and SMA (IRR = 1.627, 95%CI: 1.201–2.204, p = 0.002). In the haplotypic model, carriers of TC had increased risk of malaria (IRR = 1.068, 95%CI: 1.017–1.122, p = 0.009), while carriers of both wild-type alleles (CC) were protected against SMA (IRR = 0.679, 95%CI: 0.542–0.850, p = 0.001). Conclusion: Collectively, these findings show that the selected C5 missense mutations influence the longitudinal risk of malaria and SMA in immune-naïve children exposed to holoendemic P. falciparum transmission through a mechanism that remains to be defined.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Competing antiferromagnetic-ferromagnetic states in a d 7 Kitaev honeycomb magnet

The Kitaev model is a rare example of an analytically solvable and physically instantiable Hamiltonian yielding a topological quantum spin liquid ground state. Here we report signatures of Kitaev spin liquid physics in the honeycomb magnet Li 3 Co 2 SbO 6 , built of high-spin d 7 (Co 2+ ) ions, in contrast to the more typical low-spin d 5 electron configurations in the presence of large spin-orbit coupling. Neutron powder diffraction measurements, heat capacity, and magnetization studies support the development of a long-range antiferromagnetic order space group of C C 2/m, below T N = 11K at μ 0 H = 0T. The magnetic entropy recovered between T = 2 and 50 K is estimated to be 0.6Rln2, in good agreement with the value expected for systems close to a Kitaev quantum spin liquid state. The temperature-dependent magnetic order parameter demonstrates a β value of 0.19(3), consistent with XY anisotropy and in-plane ordering, with Ising-like interactions between layers. Further, we observe a spin-flop-driven crossover to ferromagnetic order with space group of C2/m under an applied magnetic field of μ 0 H ≈ 0.7T at T = 2K. Magnetic structure analysis demonstrates these magnetic states are competing at finite applied magnetic fields even below the spin-flop transition. Both the d 7 compass model, a quantitative comparison of the specific heat of Li 3 Co 2 SbO 6 , and related honeycomb cobaltates to the anisotropic Kitaev model further support proximity to a Kitaev spin liquid state. Furthermore, this material demonstrates the rich playground of high-spin d 7 systems for spin liquid candidates and complements known d 5 Ir- and Ru-based materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Conceptual design of DIII-D experiments to diagnose the lifetime of spin polarized fuel

Abstract In magnetic fusion experiments, the cross sections for the D-T and D- 3 He fusion reactions are increased by as much as 50% if the fuel remains spin polarized parallel to the magnetic field. The goal of this study is to assess the feasibility of lifetime measurements of spin polarization, in magnetic fusion relevant conditions, on the DIII-D tokamak using relative changes in charged fusion product (CFP) loss measurements that depend upon the differential fusion cross section d σ /dΩ. Relative measurements that capture changes in the escaping CFP pitch, poloidal, and energy distributions are studied in two realistic TRANSP calculated plasma scenarios: (a) vector-polarized 3 He and D pellets are injected into a hot hydrogen plasma to produce thermonuclear reactions, and (b) a tensor-polarized deuterium pellet is injected into an L-mode hydrogen background plasma that includes unpolarized 3 He neutral beam injection. Ideal CFP signals in both scenarios show substantial pitch sensitivity to polarization for 14.7 MeV proton detection at a poloidal angle of − 56 ∘ (on the outer wall in the ion ∇ B direction), and strong sensitivity to polarization for 3.6 MeV alpha flux detection by an array of poloidal detectors. Energy-resolved measurements of 14.7 MeV protons are also sensitive to the degree of polarization for the − 56 ∘ port in the beam-plasma scenario. A realistic assessment of CFP signals in the thermonuclear scenario show count rates in the range of 2 × 10 4 cps for pitch-resolved proton detection and 2 × 10 5 cps for alpha flux measurements. Reduced chi-squared χ r 2 calculations show polarization lifetime measurements are feasible for either proton or alpha detection of both enhanced or suppressed polarization for the thermonuclear scenario. Measurements of gamma rays produced in the weak D + 3 He → γ + 5 Li branch complement the CFP measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations

Abstract Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its target genes, which include the mtrCDE multidrug efflux transporter genes and the rpoH oxidative stress response sigma factor gene. However, the DNA-recognition mechanism of MtrR and the consensus sequence within these operators to which MtrR binds has remained unknown. In this work, we report the crystal structures of MtrR bound to the mtrCDE and rpoH operators, which reveal a conserved, but degenerate, DNA consensus binding site 5′-MCRTRCRN4YGYAYGK-3′. We complement our structural data with a comprehensive mutational analysis of key MtrR-DNA contacts to reveal their importance for MtrR-DNA binding both in vitro and in vivo. Furthermore, we model and generate common clinical mutations of MtrR to provide plausible biochemical explanations for the contribution of these mutations to multidrug resistance in N. gonorrhoeae. Collectively, our findings unveil key biological mechanisms underlying the global stress responses of N. gonorrhoeae.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Design and performance characterisation of the HAPG von Hámos Spectrometer at the High Energy Density Instrument of the European XFEL

The von Hámos spectrometer setup at the HED instrument of the European XFEL is described in detail. The spectrometer is designed to be operated primarily between 5 and 15 keV to complement the operating photon energy range of the HED instrument. Four Highly Annealed Pyrolitic Graphite (HAPG) crystals are characterised with thicknesses of 40 μm or 100 μm and radius-of-curvature 50 mm or 80 mm, in conjunction with either an ePix100 or Jungfrau detector. The achieved resolution with the 50 mm crystals, operated between 6.5 and 9 keV, matches that reported previously: ~8 eV for a thickness of 40 μm, whereas, with an 80 mm crystal of thickness 40 μm, the resolution exceeds that expected. Namely, a resolution of 2 eV is demonstrated between 5–6 keV implying a resolving power of 2800. Therefore, we posit that flatter HAPG crystals, with their high reflectivity and improved resolving power, are a powerful tool for hard x-ray scattering and emission experiments allowing unprecedented measurements of collective scattering in a single shot.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Measurements of jet observables sensitive to $\textit{b}$-quark fragmentation in $t\bar{t}$ events at the LHC with the ATLAS detector

Several observables sensitive to the fragmentation of $\textit{b}$ quarks into $\textit{b}$ hadrons are measured using 36 fb -1 of $\sqrt{s}$ = 13 TeV proton-proton collision data collected with the ATLAS detector at the LHC. Jets containing b hadrons are obtained from a sample of dileptonic $t\bar{t}$ events, and the associated set of charged-particle tracks is separated into those from the primary $\textit{pp}$ interaction vertex and those from the displaced b-decay secondary vertex. This division is used to construct observables that characterize the longitudinal and transverse momentum distributions of the $\textit{b}$ hadron within the jet. The measurements have been corrected for detector effects and provide a test of heavy-quark-fragmentation modeling at the LHC in a system where the top-quark decay products are color connected to the proton beam remnants. The unfolded distributions are compared with the predictions of several modern Monte Carlo parton-shower generators and generator tunes, and a wide range of agreement with the data is observed, with $\textit{p}$ values varying from 5 × 10 -4 to 0.98. These measurements complement similar measurements from $e^+e^-$ collider experiments in which the $\textit{b}$ quarks originate from a color singlet $Z/γ^{\ast}$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Fungal Trl1 is an essential tRNA splicing enzyme composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that convert the 2′,3′-cyclic-PO 4 and 5′-OH ends of tRNA exons into the 3′-OH,2′-PO 4 and 5′-PO 4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trifunctional Trl1 enzymes are present in most human fungal pathogens and are untapped targets for antifungal drug discovery. Mucorales species, deemed high-priority human pathogens by WHO, elaborate a noncanonical tRNA splicing apparatus in which a stand-alone monofunctional RNA ligase enzyme joins 3′-OH,2′-PO 4 and 5′-PO 4 termini. Here we identify a stand-aloneMucor circinelloidespolynucleotide kinase (MciKIN) and affirm its biological activity in tRNA splicing by genetic complementation in yeast. Recombinant MciKIN catalyzes magnesium-dependent phosphorylation of 5′-OH RNA and DNA ends in vitro. MciKIN displays a strong preference for GTP as the phosphate donor in the kinase reaction, a trait shared with the stand-alone RNA kinase homologs from Mucorales speciesRhizopus azygosporus(RazKIN) andLichtheimia corymbifera(LcoKIN) and with the kinase domains of fungal Trl1 enzymes. We report a 1.65 Å crystal structure of RazKIN in complex with GDP•Mg 2+ that illuminates the basis for guanosine nucleotide specificity.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM

Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma

Single amino acid variants (SAAVs) in protein sequences are often a direct result of single-nucleotide polymorphisms (SNPs). Certain germline SAAVs have shown biological relevance in different disease conditions but lack precise quantification in circulation, which could hinder functional investigations and progress in biomarker development. Here, we have developed a multiplexed liquid chromatography-selected reaction monitoring (LC-SRM) assay that monitors 5 wild-type and variant peptide pairs (Complement Factor B: CFB-R32Q/R32W, Clusterin: CLU-N317H, Fetuin B: FETUB-K360R, and Kininogen: KNG1-L212P) in nondepleted human plasma. The assay was optimized for imprecision, linearity, stability, and calibration assessments with CVs of under 20%. The wild-type and variant peptide pairs were characterized in a set of healthy individual plasma samples. These target identifications were also validated by SNP genotyping with more than 99% accuracy. For all protein targets, we observed significantly lower concentrations of WT species in the presence variant peptides. In CFB, the concentration of R32Q was significantly lower than its counterpart R32W variant and WT species. Furthermore, our results distinguished phenotypes of homozygosity and heterozygosity of the SAAV presence through direct concentration level characterization. These findings provide some insights into how SAAVs affect quantitative assessments of target peptides. The assay demonstrates a platform for proteogenomic analyses with potential applications in both research and clinical settings.

genetics↗

DOE OSTI2020

Four Families of Folate-independent Methionine Synthases

Abstract Although most organisms synthesize methionine from homocysteine and methyl folates, some have “core” methionine synthases that lack folate-binding domains and use other methyl donors. In vitro , the characterized core synthases use methylcobalamin as a methyl donor, but in vivo , they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.

Price, Morgan↗

DOE OSTI2021

Four families of folate-independent methionine synthases

Although most organisms synthesize methionine from homocysteine and methyl folates, some have “core” methionine synthases that lack folate-binding domains and use other methyl donors. In vitro , the characterized core synthases use methylcobalamin as a methyl donor, but in vivo , they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Confinement-Controlled Rearrangements in Dioxolane Upgrading on H-ZSM-5 Revealed by Periodic DFT

Zeolitic Brønsted acid sites catalyze carbocation rearrangements central to upgrading biomass-derived oxygenates. Here we elucidate the mechanism of dioxolane conversion to methyl ethyl ketone and isobutanal on H-ZSM-5 using periodic density functional theory on the MFI model, complemented by ab initio molecular dynamics to probe confinement effects. Dioxolane adsorption at the Brønsted site is followed by protonation-assisted ring opening to form an oxocarbenium intermediate stabilized by the deprotonated framework. From this common intermediate, selectivity is governed by two competing rearrangements, namely, the 1,2-hydride shift with a free-energy barrier of 18.05 kcal mol –1 at 498 K leading toward MEK, and the 1,2-methyl shift with a higher barrier of 25.40 kcal mol –1 leading toward isobutanal. The hydride-shift channel is kinetically preferred over the methyl-shift channel, lowering the isobutanal/MEK ratio below the 3:1 limit expected for equal branching. Adsorption thermodynamics further indicate stronger stabilization of MEK than isobutanal within ZSM-5 channels, suggesting that confinement-controlled binding can bias product distributions in addition to intrinsic rearrangement barriers. These results highlight how Brønsted acidity and pore confinement jointly shape the rearrangement landscape in MFI zeolites.

adsorption↗

DOE OSTI2021

Tuning spin–orbit coupling in (6,5) single-walled carbon nanotube doped with sp 3 defects

Single-walled carbon nanotubes (SWCNTs) containing sp 3 defects are a promising class of optoelectronic materials with bright photoluminescence and demonstrated single-photon emission. Using density functional theory simulations, complemented by measurements, we investigate the electronic structure of a series of quantum defects attached to (6,5) SWCNT with the goal of tuning the spin–orbit coupling by introduction of a heavy atom in the defect structure. We characterize the ground state electronic and spin properties of four synthesized and three potential defects on the tube and find that all of the synthesized defects considered introduce a localized midgap defect-centered state containing a single electron, ≈0.2–0.3 eV above the valence band. The spin density is located at the sp 3 defect site with negligible spin–orbit coupling even with the presence of a Pd atom. Three additional functional groups were tested via computation to increase spin localization near the metal, thereby increasing spin–orbit coupling. We predict that only the chlorodiphosphanepalladium(II)– [Cl(PH 3 ) 2 Pd(II)–] defect results in increased spin–orbit splitting of the defect state and the conduction band associated with the pristine-like SWCNT, a measure of the spin–orbit coupling of excited state transitions. This study suggests that for unpassivated sp 3 defects in (6,5) SWCNT, forming a direct bond between a heavy atom and the sp 3 carbon allows for tuning of spin–orbit coupling.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Room-temperature in-plane ferromagnetism in Co-substituted Fe 5 GeTe 2 investigated by magnetic x-ray spectroscopy and microscopy

The exploration of two-dimensional (2D) van der Waals ferromagnets has revealed intriguing magnetic properties with significant potential for spintronics applications. In this study, we examine the magnetic properties of Co-doped Fe 5 GeTe 2 using x-ray photoemission electron microscopy (XPEEM) and x-ray magnetic circular dichroism (XMCD), complemented by density functional theory calculations. Our XPEEM measurements reveal that the Curie temperature (T c ) of a bilayer of (Co x Fe 1-x ) 5-δ GeTe 2 (with x = 0.28) reaches ∼300 K—a notable enhancement over most 2D ferromagnets in the ultrathin limit. Interestingly, the T c shows only a small dependence on film thickness (bulk T c ≈ 340 K), in line with the observed in-plane (IP) magnetic anisotropy and robust IP exchange coupling. XMCD measurements indicate that the spin moments for both Fe and Co are significantly reduced compared to the theoretical values. These insights highlight the potential of Co-doped Fe 5 GeTe 2 for stable, high-temperature ferromagnetic applications in 2D materials.

(Co0.28Fe0.72)5GeTe2↗

DOE OSTI2024

Reduced-order condensed-phase kinetic models for polyethylene, polypropylene and polystyrene thermochemical recycling

Thermochemical recycling of plastic waste (PW) into chemicals and energy vectors requires coupling particle and reactor-scale simulations to accurate condensed phase pyrolysis mechanisms for each constituent. This work proposes a methodology to derive reduced-order condensed-phase kinetic models from validated semi-detailed kinetic mechanisms. Two types of kinetic models are obtained for polyethylene (PE), polypropylene (PP) and polystyrene (PS): reduced semi-detailed models and multi-step fully lumped ones. These families offer different compromises between accuracy and computational cost. The former employ 50–100 gas + liquid species and describe both the radical degradation and the detailed carbon distribution of the products. Conversely, the latter involves 5–10 species per polymer tracking only the main petroleum cuts. The kinetic mechanisms are complemented by the definition of thermochemical properties of gas, liquid, and solid-phase species, accounting for phase-transitions through pseudo-chemical reactions. Model validations are performed by comparison with experimental data and the original semi-detailed mechanisms in terms of mass loss, heat fluxes and product distribution profiles. The resulting CHEMKIN-like condensed-phase models are attached as Supplementary Material and as a GitHub repository. Extending the proposed approach to other polymers and coupling it with existing subsets in the CRECK kinetic framework (e.g., biomass, PVC, PET) offers a powerful tool to model thermochemical recycling of PW and biomass/PW mixtures.

kinetics↗

DOE OSTI2026

AI-driven neutrino diagnostics and radiation-hard beam instrumentation for next-generation neutrino experiments

The Long Baseline Neutrino Facility (LBNF) at Fermilab will deliver a high-intensity, multi-megawatt neutrino beam to the Deep Underground Neutrino Experiment (DUNE), enabling precision tests of the three-neutrino paradigm, CP violation searches, neutrino mass ordering determination, and supernova neutrino studies. To accelerate DUNE’s physics reach and ensure robust beam operations, we propose an integrated AI-driven framework with real-time diagnostics and radiation-hardened instrumentation. At its core is a Real-Time Beam Integrity Monitor using a physics-informed Digital Twin. By reconstructing pion phase space from muon profiles and exploiting magnetic horn optic linearity, it enables spill-by-spill beam correction and flux stabilization. By using this approach, flux-related systematics could be reduced from 5% to 1%, potentially accelerating the discovery of CP violations by four to six years. Complementing this, a US–Japan R&D effort will deploy a LAPPD-based muon monitor in the NuMI beamline. ToF measurements can be acquired with picosecond precision using this radiation-hard system, enhancing sensitivity to horn chromatic effects. Simulations confirm strong response to these effects. ML models predict beam quality and horn current to sub-percent accuracy from muon data, enhancing anomaly detection and stability. This scalable, AI-enabled strategy improves beam fidelity, reduces systematics, and sets a new standard for high-power accelerator operations.

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

DOE OSTI2025

AI-driven neutrino diagnostics and radiation-hard beam instrumentation for next-generation neutrino experiments

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

DOE OSTI2026

Plasmon-Assisted Electrochemical Epoxidation using Water as an Oxidant

Olefin epoxidation, an important industrial reaction, often uses hazardous oxidants, causing challenges in waste disposal. Here, we demonstrate the use of water as an oxidant by a plasmon-assisted electrochemical strategy. The electrocatalyst is comprised of a hybrid of a water oxidation catalyst, manganese oxide, and plasmonic gold nanoparticles. Visible-light irradiation of the electrocatalyst enhanced the epoxidation of 4-styrenesulfonate 5-fold as compared to dark conditions at the same temperature. From electrochemical analyses conducted under plasmon excitation conditions, complemented by real-time time-dependent density functional tight binding simulations, it is found that the plasmonic boost of the electrochemical styrene epoxidation is due to energetic holes generated by the excitation of localized surface plasmon resonances of gold nanoparticles. These photogenerated holes activate adsorbed water for oxidation and enhance the binding of 4-styrenesulfonate at interfacial sites. Here, this work demonstrates a proof of concept and establishes the mechanistic basis for plasmon-assisted activation of water as an O atom source for electrochemical epoxidations.

Gold↗